Format for Individual Target pages (copy this list to new Target page and then fill in for your target):
*Target (protein/gene name): Tyrosine-protein phosphatase yopH *NCBI Gene # or RefSeq#: YPPY56_4860 *Protein ID (NP or XP #) or Wolbachia#: P15273 *Organism (including strain): Yersinia enterocolitica Etiologic Risk Group (see link below):
*Background/Disease Information (sort of like the Intro to your Mini Research Write up): Protein tyrosine phosphatases play a role in regulation of normal and pathological processes such as cell proliferation, differentiation, metabolism, and the survival of human diseases such as cancer and diabetes. Tyrosine-protein phosphatase yopH main function is to dephosphorylate host-proteins in Yersinia pathogenesis and contributes to the resistant’s of phagocytosis by peritoneal macrophages.
Essentiality of this protein: Complex of proteins?: Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
*EC#: 3.1.3.48 Link to BRENDA EC# page: --Show screenshot of BRENDA enzyme mechanism schematic Fig 1: Reaction catalyzed by protein-tyrosine-phosphatase (3.1.3.48)
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents): -- link to Sigma (or other company) page for assay (see Sigma links below) -- -or link (or citation) to paper that contains assay information -- links to assay reagents (substrates) pages. --- List cost and quantity of substrate reagents, supplier, and catalog #
Structure Available (PDB or Homology model) -- PDB # or closest PDB entry if using homology model: 3BLT -- For Homology Model option: ---- Query Coverage: 100% ---- Max % Identities: 100% ---- % Positives: 100% ---- Chain used for homology: ---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
Current Inhibitors:http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?tag=pol&submit=Search&target=tyrosine-protein%20phosphatase%20yoph&polymerid=50003487 Expression Information (has it been expressed in bacterial cells): Mostly like no transmembrane protein - no possible model found according to TMPred results. Purification Method:http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Datasheet/5/t1196dat.pdf Image of protein (PyMol with features delineated and shown separately): *Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
RERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS *length of your protein in Amino Acids: 305 residues Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 50869.3 Molar Extinction coefficient of your protein at 280 nm wavelength:
Ext. coefficient 19285 Abs 0.1% (=1 g/l) 0.379, assuming all pairs of Cys residues form cystine.
Ext. coefficient 18910 Abs 0.1% (=1 g/l) 0.372, assuming all Cys residues are reduced. TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it. *CDS Gene Sequence (paste as text only): *GC% Content for gene: *CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only): *GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now) Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers): (link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**
Format for Individual Target pages (copy this list to new Target page and then fill in for your target):
*Target (protein/gene name): Tyrosine-protein phosphatase yopH*NCBI Gene # or RefSeq#: YPPY56_4860
*Protein ID (NP or XP #) or Wolbachia#: P15273
*Organism (including strain): Yersinia enterocolitica
Etiologic Risk Group (see link below):
*Background/Disease Information (sort of like the Intro to your Mini Research Write up):
Protein tyrosine phosphatases play a role in regulation of normal and pathological processes such as cell proliferation, differentiation, metabolism, and the survival of human diseases such as cancer and diabetes. Tyrosine-protein phosphatase yopH main function is to dephosphorylate host-proteins in Yersinia pathogenesis and contributes to the resistant’s of phagocytosis by peritoneal macrophages.
Link to TDR Targets page (if present): No page for yopH on TDR Targets
Link to Gene Database page (NCBI, EuPath databases -e.g. TryTryp, PlasmoDB, etc - or PATRIC, etc.):
http://www.rcsb.org/pdb/explore/explore.do?structureId=3BLT
Essentiality of this protein:
Complex of proteins?:
Druggable Target (list number or cite evidence from a paper/database showing druggable in another organism):
*EC#: 3.1.3.48
Link to BRENDA EC# page:
-- Show screenshot of BRENDA enzyme mechanism schematic
Fig 1: Reaction catalyzed by protein-tyrosine-phosphatase (3.1.3.48)
Enzyme Assay information (spectrophotometric, coupled assay ?, reagents):
-- link to Sigma (or other company) page for assay (see Sigma links below)
-- -or link (or citation) to paper that contains assay information
-- links to assay reagents (substrates) pages.
--- List cost and quantity of substrate reagents, supplier, and catalog #
Structure Available (PDB or Homology model)
-- PDB # or closest PDB entry if using homology model: 3BLT
-- For Homology Model option:
---- Query Coverage: 100%
---- Max % Identities: 100%
---- % Positives: 100%
---- Chain used for homology:
---- Show pairwise alignment of your BLASTP search in NCBI against the PDB
<span style="background-color: #ffffff; color: #222222; font-size: 12px;">Query 1 RERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGG 60 RERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGG Sbjct 2 RERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGG 61 Query 61 EKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLA 120 EKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLA Sbjct 62 EKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLA 121 Query 121 VLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKT 180 VLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKT Sbjct 122 VLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKT 181 Query 181 ISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHC 240 ISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHC Sbjct 182 ISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHC 241 Query 241 RAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGR 300 RAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGR Sbjct 242 RAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGR 301 Query 301 PLLNS 305 PLLNS Sbjct 302 PLLNS 306</span>Current Inhibitors: http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?tag=pol&submit=Search&target=tyrosine-protein%20phosphatase%20yoph&polymerid=50003487
Expression Information (has it been expressed in bacterial cells): Mostly like no transmembrane protein - no possible model found according to TMPred results.
Purification Method: http://www.sigmaaldrich.com/content/dam/sigma-aldrich/docs/Sigma/Datasheet/5/t1196dat.pdf
Image of protein (PyMol with features delineated and shown separately):
*Amino Acid Sequence (paste as text only - not as screenshot or as 'code'):
RERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS
*length of your protein in Amino Acids: 305 residues
Molecular Weight of your protein in kiloDaltons using the Expasy ProtParam website: 50869.3
Molar Extinction coefficient of your protein at 280 nm wavelength:
Ext. coefficient 19285 Abs 0.1% (=1 g/l) 0.379, assuming all pairs of Cys residues form cystine.
Ext. coefficient 18910 Abs 0.1% (=1 g/l) 0.372, assuming all Cys residues are reduced.
TMpred graph Image (http://www.ch.embnet.org/software/TMPRED_form.html). Input your amino acid sequence to it.
*CDS Gene Sequence (paste as text only):
*GC% Content for gene:
*CDS Gene Sequence (codon optimized) - copy from output of Primer Design Protocol (paste as text only):
*GC% Content for gene (codon optimized):
Do Not Need this info for Spring (but still copy these lines to your Target page for now)
Primer design results for pNIC-Bsa4 cloning (list seqeunces of all of your ~40 nt long primers):
(link to DNA Works output text file - that should be saved in your Google Docs folder after you did the primer design protocol)
-- Ask a mentor, Dr. B, or a fellow researcher -how to link a GDocs file if you are not sure how to.
Primer design results for 'tail' primers (this is just 2 sequences):
**